Labor chief whip Joel Fitzgibbon warned on Tuesday that the commission would be a "big and slow-moving beast".
"The royal commission could take a decade," he told ABC radio. "And make no mistake, it will cause trauma for many individuals and organisations."
The commission will cover all religious institutions, state-based organisations, schools and not-for-profit groups such as scouts and sporting clubs.
Prime Minister Julia Gillard announced the inquiry on Monday, following fresh allegations that the Catholic Church and police covered up abuse in the Hunter region of NSW.
But Australia's most senior Catholic, Cardinal George Pell, hopes the wide-ranging royal commission will actually stop a "smear campaign" against his church.
"We are not interested in denying the extent of misdoing in the Catholic Church," he told reporters in Sydney. (But) we object to it being exaggerated. We object to being described as the only cab on the rank."
Cardinal Pell questioned whether victims were helped by "continuing furore in the press".
He also asked if the police had the resources to deal with current abuse as well as historical cases.
Federal Opposition Leader Tony Abbott backed the church's leadership to co-operate fully with the royal commission.
Mr Abbott, a high-profile Catholic himself, acknowledged there had been "shattering" revelations about a number of institutions over the years "including my own church".
"I know the current leadership of the church is determined to get to the bottom of this," he told reporters in Brisbane.
A number of legal experts have warned the royal commission will be overwhelmed by its breadth.
The senior counsel who assisted the Victorian bushfires royal commission, Jack Rush, said, "It's very important in a royal commission that things are done quickly."
But Ms Gillard insists the commission will run "as long as it takes to do it right".
"We should not set artificial limits on getting this done properly," she told reporters in Perth.
Acting Families Minister Brendan O'Connor argued Labor would be criticised if it "restricted the terms of reference to such an extent they can not inquire into this matter fully".
Shadow attorney-general George Brandis believes that while an indicative time limit could be set, it shouldn't be enforced.
"If the royal commissioner uncovers avenues of inquiry that need to be explored, well they just have to be explored," he told Sky News.
Independent senator Nick Xenophon argues the commission should be given a two-year deadline.
"It can't drag on for nine or 10 years as the Irish commission of inquiry did," he told ABC television.
However, the man who ran that Irish inquiry has warned against an early deadline.
"I would be backing off that," High Court Justice Sean Ryan told News Ltd. "The government will give an awful lot of thought to selecting the right people to conduct the inquiry ... and I would trust those people to make that call."